The city is built primarily on bluffs and terraces that rise 100–200 feet (30–61 m) above the western banks of the Mississippi River, just south of the Missouri-Mississippi confluence. Much of the area is a fertile and gently rolling prairie that features low hills and broad, shallow valleys. Both the Mississippi River and the Missouri River have cut large valleys with wide flood plains.

Limestone and dolomite of the Mississippianepoch underlies the area and much of the city is a karst area, with numerous sinkholes and caves, although most of the caves have been sealed shut; many springs are visible along the riverfront. Significant deposits of coal, brickclay, and millerite ore were once mined in the city, and the predominant surface rock, the St. Louis Limestone, is used as dimension stone and rubble for construction.

The St. Louis Geologic fault is exposed along the bluffs and was the source of several historic minor earthquakes; it is part of the St. Louis Anticline which has some petroleum and natural gas deposits outside of the city. St. Louis is also just north of the New Madrid Seismic Zone which in 1811–12 produced a series of earthquakes that are the largest known in the contiguous United States. Seismologists estimate 90% probability of a magnitude 6.0 earthquake by 2040 and 7-10% probability of a magnitude 8.0,[2] such tremors could create significant damage across a large region of the central U.S. including St. Louis.

Near the southern boundary of the City of St. Louis (separating it from St. Louis County) is the River des Peres, virtually the only river or stream within the city limits that is not entirely underground. Most of River des Peres was either channelized or put underground in the 1920s and early 1930s. The lower section of the river was the site of some of the worst flooding of the Great Flood of 1993.

The city is divided into 79 neighborhoods. The divisions have no legal standing, although some neighborhood associations administer grants or hold veto power over historic-district development. Nevertheless, the social and political influence of neighborhood identity is profound. Some hold avenues of massive stone edifices built as palaces for heads of state visiting the 1904 World's Fair. Others offer tidy working-class bungalows, loft districts, or areas hard-hit by social problems and unemployment. Many of them have retained - quite consciously and deliberately - a camaraderie that is missing from many American towns today.

The climate is humidsubtropical (Köppen: Cfa), but all around Greater St. Louis has a humid continental climate (Dfa) through the USA isoterm, with a winter that sustains in the coldest month temperatures below 0 ° C more easily, clear evidence of an island of urban heat, which in the future may cover an even larger area and agglutinate cities and villages to the south.[4] It straddles the border between USDA Plant Hardiness Zones 6B and 7A,[5] indicating the coldest temperature of the year is typically around 0 °F (−18 °C). With neither large mountains nor large bodies of water to moderate its temperature, it is subject to both cold Arctic air and hot, humid tropical air from the Gulf of Mexico. The city has four distinct seasons. Spring is the wettest season and produces severe weather ranging from tornadoes to winter storms. Summers are hot and humid; temperatures of 90 °F (32 °C) or higher occur 43 days a year.[6] The average window for such temperatures is May 19 thru September 14.[3]

Fall is mild with lower humidity and can produce intermittent bouts of heavy rainfall with the first freeze of the season on average falling on November 2 (the last on average falls on April 3); the first measurable (0.1 inches (0.25 cm)) snow, often not counting flurries, on average occurs on December 4 (the last on average falls on March 17). Winters can be cold and snowy with temperatures frequently below freezing. Winter storm systems, such as Alberta clippers and Panhandle hooks, can bring days of heavy freezing rain, ice pellets, and snowfall.

The average annual temperature recorded at nearby Lambert–St. Louis International Airport, is 57.1 °F (13.9 °C), and average precipitation is about 41.0 inches (1,040 mm). The daily average temperature in July is 80.0 °F (26.7 °C), while in January it is 31.8 °F (−0.1 °C), although this varies from year to year. Both 100 °F (37.8 °C) and 0 °F (−17.8 °C) temperatures can be seen on an average 2 or 3 days per year. The official record low is −22 °F (−30 °C) on January 5, 1884, although there were unofficial readings of −23 °F (−31 °C) on January 29, 1873; and the record high is 115 °F (46 °C) on July 14, 1954;[7] the coldest high on record was −5 °F (−21 °C) on December 24, 1983, while, conversely, the warmest low on record was 86 °F (30 °C) on July 25, 2012 and July 24, 1901. July 2012 was the hottest month in the 138-year recorded weather temperatures in St. Louis history starting in 1874, with an average daily temperature of 88.1 °F (31.2 °C).[7]

Winter (December through February) is the driest season, with an average 7.5 in (191 mm) of precipitation. The average seasonal snowfall is 18.2 inches (46 cm), typically falling from December to March. The heaviest one-day snowfall total was 12.8 in (32.5 cm) on February 26, 1906. Spring (March through May), is typically the wettest season, with 11.7 in (297 mm) of precipitation; however, the heaviest 24-hour rainfall total was 6.85 in (174.0 mm) on August 20, 1915. Dry spells lasting one to two weeks are common during the growing seasons.

St. Louis experiences thunderstorms 48 days a year on average.[8] Especially in the spring, these storms can often be severe, with high winds, large hail and tornadoes. Lying within the hotbed of Tornado Alley, St. Louis reigns as one of the most frequently tornadic metropolitan areas, and has an extensive history of particularly damaging tornadoes. Severe flooding, such as the Great Flood of 1993, may occur in spring and summer; the (often rapid) melting of thick snow cover upstream either the Missouri or Mississippi Rivers can contribute to springtime flooding.

Some late autumns feature the warm weather known as Indian summer; some years see roses in bloom as late as early December.

Before the founding of the city, the area was prairie and open forest maintained by burning by Native Americans. Trees are mainly oak, maple, and hickory, similar to the forests of the nearby Ozarks; common understory trees include eastern redbud, serviceberry, and flowering dogwood. Riparian areas are forested with mainly American sycamore. Most of the residential area of the city is planted with large native shade trees. The largest native forest area is found in Forest Park. In autumn, the changing color of the trees is notable. Most species here are typical of the Eastern Woodland, although numerous decorative non-native species are found; the most notable invasive species is Japanese honeysuckle, which is actively removed from some parks.

Frogs are commonly found in the springtime, especially after extensive wet periods. Common species include the American toad and species of chorus frogs, commonly called "spring peepers" that are found in nearly every pond. Some years have outbreaks of cicadas or ladybugs. Mosquitos and houseflies are common insect nuisances; because of this, windows are nearly universally fitted with screens, and "screened-in" porches are common in homes of the area. Populations of honey bees have sharply declined in recent years, and numerous species of pollinator insects have filled their ecological niche.

^Mean monthly maxima and minima (i.e. the highest and lowest temperature readings during an entire month or year) calculated based on data at said location from 1981 to 2010.

^Official records for St. Louis were kept at the Weather Bureau Office from January 1874 to December 1892, Eads Bridge from January 1893 to December 1929, and at Lambert–St. Louis Int'l since January 1930.[9]